Colorimetric detection of caspase 3 activity and reactive oxygen derivatives: Potential early indicators of thermal stress in corals

© 2016 Mickael Ros et al. There is an urgent need to develop and implement rapid assessments of coral health to allow effective adaptive management in response to coastal development and global change. There is now increasing evidence that activation of caspase-dependent apoptosis plays a key role during coral bleaching and subsequent mortality. In this study, a "clinical" approach was used to assess coral health by measuring the activity of caspase 3 using a commercial kit. This method was first applied while inducing thermal bleaching in two coral species, Acropora millepora and Pocillopora damicornis. The latter species was then chosen to undergo further studies combining the detection of oxidative stress-related compounds (catalase activity and glutathione concentrations) as well as caspase activity during both stress and recovery phases. Zooxanthellae photosystem II (PSII) efficiency and cell density were measured in parallel to assess symbiont health. Our results demonstrate that the increased caspase 3 activity in the coral host could be detected before observing any significant decrease in the photochemical efficiency of PSII in the algal symbionts and/or their expulsion from the host. This study highlights the potential of host caspase 3 and reactive oxygen species scavenging activities as early indicators of stress in individual coral colonies

Arabinogalactan-proteins and the research challenges for these enigmatic plant cell surface proteoglycans

Arabinogalactan-proteins (AGPs) are complex glycoconjugates that are commonly found at the cell surface and in secretions of plants. Their location and diversity of structures have made them attractive targets as modulators of plant development but definitive proof of their direct role(s) in biological processes remains elusive. Here we overview the current state of knowledge on AGPs, identify key challenges impeding progress in the field and propose approaches using modern bioinformatic, (bio)chemical, cell biological, molecular and genetic techniques that could be applied to redress these gaps in our knowledge

Regulation of Meristem Morphogenesis by Cell Wall Synthases in Arabidopsis.

The cell walls of the shoot apical meristem (SAM), containing the stem cell niche that gives rise to the above-ground tissues, are crucially involved in regulating differentiation. It is currently unknown how these walls are built and refined or their role, if any, in influencing meristem developmental dynamics. We have combined polysaccharide linkage analysis, immuno-labeling, and transcriptome profiling of the SAM to provide a spatiotemporal plan of the walls of this dynamic structure. We find that meristematic cells express only a core subset of 152 genes encoding cell wall glycosyltransferases (GTs). Systemic localization of all these GT mRNAs by in situ hybridization reveals members with either enrichment in or specificity to apical subdomains such as emerging flower primordia, and a large class with high expression in dividing cells. The highly localized and coordinated expression of GTs in the SAM suggests distinct wall properties of meristematic cells and specific differences between newly forming walls and their mature descendants. Functional analysis demonstrates that a subset of CSLD genes is essential for proper meristem maintenance, confirming the key role of walls in developmental pathways.V.C. is in receipt of a Thailand Research Fund (TRF) grant for New Researcher (Grant Number TRG5880067), and a Research Supplement grant from Faculty of Science, Mahidol University. CB, MSD and AB acknowledge the support of the ARC Centre of Excellence in Plant Cell Walls, Australia (Grant Number CE110001007). EMM acknowledges support from the Gatsby Charitable Trust through Fellowships GAT3272/C and GAT3273-PR1, the Howard Hughes Medical Institute, the Gordon and Betty Moore Foundation (through Grant GBMF3406) and the US Department of Energy (through award DE-FG02-99ER13873). AP acknowledges support of the EU Marie-Curie FP7 COFUND People Programme through the award of an AgreenSkills grant no. 267196. RW acknowledges support from the Leverhulme Trust (Grant RPG-2015-285).This is the author accepted manuscript. The final version is available from Cell Press via http://dx.doi.org/10.1016/j.cub.2016.04.02

Metabolic adaptation via regulated enzyme degradation in the pathogenic yeast Candida albicans

The virulence of Candida albicans is dependent upon fitness attributes as well as virulence factors. These attributes include robust stress responses and metabolic flexibility. The assimilation of carbon sources is important for growth and essential for the establishment of infections by C. albicans. Previous studies showed that the C. albicans ICL1 genes, which encode the glyoxylate cycle enzymes isocitratelyase are required for growth on non-fermentable carbon sources such as lactate and oleic acid and were repressed by 2% glucose. In contrast to S. cerevsiae, the enzyme CaIcl1 was not destabilised by glucose, resulting with its metabolite remaining at high levels. Further glucose addition has caused CaIcl1 to lose its signal and mechanisms that trigger destabilization in response to glucose. Another purpose of this study was to test the stability of the Icl1 enzyme in response to the dietary sugars, fructose, and galactose. In the present study, the ICL1 mRNAs expression was quantified using Quantitative Real Time PCR, whereby the stability of protein was measured and quantified using Western blot and phosphoimager, and the replacing and cloning of ICL1 ORF by gene recombination and ubiquitin binding was conducted via co-immuno-precipitation. Following an analogous experimental approach, the analysis was repeated using S. cerevisiaeas a control. Both galactose and fructose were found to trigger the degradation of the ICL1 transcript in C. albicans. The Icl1 enzyme was stable following galactose addition but was degraded in response to fructose. C. albicans Icl1 (CaIcl1) was also subjected to fructose-accelerated degradation when expressed in S. cerevisiae, indicating that, although it lacks a ubiquitination site, CaIcl1 is sensitive to fructose-accelerated protein degradation. The addition of an ubiquitination site to CaIcl1 resulted in this enzyme becoming sensitive to galactose-accelerated degradation and increases its rate of degradation in the presence of fructose. It can be concluded that ubiquitin-independent pathways of fructose-accelerated enzyme degradation exist in C. albicans

Photosynthesis–irradiance parameters of marine phytoplankton: synthesis of a global data set

The photosynthetic performance of marine phytoplankton varies in response to a variety of factors, environmental and taxonomic. One of the aims of the MArine primary Production: model Parameters from Space (MAPPS) project of the European Space Agency is to assemble a global database of photosynthesis– irradiance (P-E) parameters from a range of oceanographic regimes as an aid to examining the basin-scale variability in the photophysiological response of marine phytoplankton and to use this information to improve the assignment of P-E parameters in the estimation of global marine primary production using satellite data. The MAPPS P-E database, which consists of over 5000 P-E experiments, provides information on the spatiotemporal variability in the two P-E parameters (the assimilation number, PB m , and the initial slope, �B, where the superscripts B indicate normalisation to concentration of chlorophyll) that are fundamental inputs for models (satellite-based and otherwise) of marine primary production that use chlorophyll as the state variable. Qualitycontrol measures consisted of removing samples with abnormally high parameter values and flags were added to denote whether the spectral quality of the incubator lamp was used to calculate a broad-band value of �B. The MAPPS database provides a photophysiological data set that is unprecedented in number of observations and in spatial coverage. The database will be useful to a variety of research communities, including marine ecologists,biogeochemical modellers, remote-sensing scientists and algal physiologists

Functional Specialization of Cellulose Synthase Isoforms in a Moss Shows Parallels with Seed Plants

The secondary cell walls of tracheary elements and fibers are rich in cellulose microfibrils that are helically oriented and laterally aggregated. Support cells within the leaf midribs of mosses deposit cellulose-rich secondary cell walls, but their biosynthesis and microfibril organization have not been examined. Although the Cellulose Synthase (CESA) gene families of mosses and seed plants diversified independently, CESA knockout analysis in the moss Physcomitrella patens revealed parallels with Arabidopsis (Arabidopsis thaliana) in CESA functional specialization, with roles for both subfunctionalization and neofunctionalization. The similarities include regulatory uncoupling of the CESAs that synthesize primary and secondary cell walls, a requirement for two or more functionally distinct CESA isoforms for secondary cell wall synthesis, interchangeability of some primary and secondary CESAs, and some CESA redundancy. The cellulose-deficient midribs of ppcesa3/8 knockouts provided negative controls for the structural characterization of stereid secondary cell walls in wild type P. patens. Sum frequency generation spectra collected from midribs were consistent with cellulose microfibril aggregation, and polarization microscopy revealed helical microfibril orientation only in wild type leaves. Thus, stereid secondary walls are structurally distinct from primary cell walls, and they share structural characteristics with the secondary walls of tracheary elements and fibers. We propose a mechanism for the convergent evolution of secondary walls in which the deposition of aggregated and helically oriented microfibrils is coupled to rapid and highly localized cellulose synthesis enabled by regulatory uncoupling from primary wall synthesis

Primary Production, an Index of Climate Change in the Ocean: Satellite-Based Estimates over Two Decades

Primary production by marine phytoplankton is one of the largest fluxes of carbon on our planet. In the past few decades, considerable progress has been made in estimating global primary production at high spatial and temporal scales by combining in situ measurements of primary production with remote-sensing observations of phytoplankton biomass. One of the major challengesinthisapproachliesintheassignmentoftheappropriatemodelparametersthatdefinethe photosynthetic response of phytoplankton to the light field. In the present study, a global database of in situ measurements of photosynthesis versus irradiance (P-I) parameters and a 20-year record of climatequalitysatelliteobservationswereusedtoassessglobalprimaryproductionanditsvariability with seasons and locations as well as between years. In addition, the sensitivity of the computed primaryproductiontopotentialchangesinthephotosyntheticresponseofphytoplanktoncellsunder changing environmental conditions was investigated. Global annual primary production varied from 38.8 to 42.1 Gt C yr−1 over the period of 1998–2018. Inter-annual changes in global primary production did not follow a linear trend, and regional differences in the magnitude and direction of change in primary production were observed. Trends in primary production followed directly from changes in chlorophyll-a and were related to changes in the physico-chemical conditions of the water column due to inter-annual and multidecadal climate oscillations. Moreover, the sensitivity analysis in which P-I parameters were adjusted by±1 standard deviation showed the importance of accurately assigning photosynthetic parameters in global and regional calculations of primary production. TheassimilationnumberoftheP-Icurveshowedstrongrelationshipswithenvironmental variables such as temperature and had a practically one-to-one relationship with the magnitude of change in primary production. In the future, such empirical relationships could potentially be used for a more dynamic assignment of photosynthetic rates in the estimation of global primary production. RelationshipsbetweentheinitialslopeoftheP-Icurveandenvironmentalvariableswere more elusive

A database of chlorophyll a in Australian waters

© The Author(s) 2018. Chlorophyll a is the most commonly used indicator of phytoplankton biomass in the marine environment. It is relatively simple and cost effective to measure when compared to phytoplankton abundance and is thus routinely included in many surveys. Here we collate 173, 333 records of chlorophyll a collected since 1965 from Australian waters gathered from researchers on regular coastal monitoring surveys and ocean voyages into a single repository. This dataset includes the chlorophyll a values as measured from samples analysed using spectrophotometry, fluorometry and high performance liquid chromatography (HPLC). The Australian Chlorophyll a database is freely available through the Australian Ocean Data Network portal (https://portal.aodn.org.au/). These data can be used in isolation as an index of phytoplankton biomass or in combination with other data to provide insight into water quality, ecosystem state, and relationships with other trophic levels such as zooplankton or fish

Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences 108 (2011): 4352-4357, doi:10.1073/pnas.1016106108.Harmful algal blooms (HABs) cause significant economic and ecological damage worldwide. Despite considerable efforts, a comprehensive understanding of the factors that promote these blooms has been lacking because the biochemical pathways that facilitate their dominance relative to other phytoplankton within specific environments have not been identified. Here, biogeochemical measurements demonstrated that the harmful 43 Aureococcus anophagefferens outcompeted co-occurring phytoplankton in estuaries with elevated levels of dissolved organic matter and turbidity and low levels of dissolved inorganic nitrogen. We subsequently sequenced the first HAB genome (A. anophagefferens) and compared its gene complement to those of six competing phytoplankton species identified via metaproteomics. Using an ecogenomic approach, we specifically focused on the gene sets that may facilitate dominance within the environmental conditions present during blooms. A. anophagefferens possesses a larger genome (56 mbp) and more genes involved in light harvesting, organic carbon and nitrogen utilization, and encoding selenium- and metal-requiring enzymes than competing phytoplankton. Genes for the synthesis of microbial deterrents likely permit the proliferation of this species with reduced mortality losses during blooms. Collectively, these findings suggest that anthropogenic activities resulting in elevated levels of turbidity, organic matter, and metals have opened a niche within coastal ecosystems that ideally suits the unique genetic capacity of A. anophagefferens and thus has facilitated the proliferation of this and potentially other HABs.Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Efforts were also supported by awards from New York Sea Grant to Stony Brook University, National Oceanic and Atmospheric Administration Center for Sponsored Coastal Ocean Research award #NA09NOS4780206 to Woods Hole Oceanographic Institution, NIH grant GM061603 to Harvard University, and NSF award IOS-0841918 to The University of Tennessee

Selection of Suitable Reference Genes for RT-qPCR Analyses in Cyanobacteria

Cyanobacteria are a group of photosynthetic prokaryotes that have a diverse morphology, minimal nutritional requirements and metabolic plasticity that has made them attractive organisms to use in biotechnological applications. The use of these organisms as cell factories requires the knowledge of their physiology and metabolism at a systems level. For the quantification of gene transcripts real-time quantitative polymerase chain reaction (RT-qPCR) is the standard technique. However, to obtain reliable RT-qPCR results the use and validation of reference genes is mandatory. Towards this goal we have selected and analyzed twelve candidate reference genes from three morphologically distinct cyanobacteria grown under routinely used laboratory conditions. The six genes exhibiting less variation in each organism were evaluated in terms of their expression stability using geNorm, NormFinder and BestKeeper. In addition, the minimum number of reference genes required for normalization was determined. Based on the three algorithms, we provide a list of genes for cyanobacterial RT-qPCR data normalization. To our knowledge, this is the first work on the validation of reference genes for cyanobacteria constituting a valuable starting point for future works